Hi,
The last ship I captured, a Behemoth Vanguard, a few days ago, I only just got around to looking at and I've updated the mod since.
Basically, at the end of last month, I boarded the ship and assigned one of the Marines as the new Captain. I then sent it, and my Marine carrying ship Buffalo, to dock at my HQ. Loading the game this evening - now with the latest version of Better Piracy - I ordered the Buffalo to transfer the Marines back from the Behemoth. However, the moment I did this, the Behemoth went yellow (rather than green) on the Map, and now only shows on the Object List view, and not the Property Owned view. I can still order it around just fine though.
Getting on the ship myself, I look at the Captain (an Ex-Marine) and while he shows green, his faction is "Teladi Company" not me. Yet I can still re-assign him and order him around as if he is mine. If I pilot the ship myself, the Behemoth goes Green on the map and is once again shown in my Property Owned list. Get out of the Pilots station, letting the Captain take over again, and the ship goes Yellow once more.
If I unassign the Captain - so there's no captain and an "assign Captain" mission is generated, the ship goes yellow again. I'm about to try assigning a NEW Captain I just hired...
... The ships remains yellow and the new Captain shows as Teladi Company, just like the old one did.
I can still use this ship, but something is a bit broken here. Any ideas what might have caused this? It's a totally new one for me.
Edit: I examined the Save and it appears the ship has applied a "Disguise" as Teladi. It was an SCA ship, but obviously fully revealed as SCA when I captured it, but it's tried to disguise its self again the moment I transfer the Marines off. I may save-edit to try to fix it.
Edit 2: I made a post about it in the main forum
here It did resolve its self in the end, I describe how in that thread. Random vanilla gremlin I expect, rather than linked to your mod. Thought it worth sharing here though, just in case
Scoob.